It largely depends on the verb used. If you use "take", then no preposition is necessary at all - e.g. "I took the plane/train/bus/boat to the city".

If you're determined to use the verb "to go" (or one of its synonyms, like "to travel"), then using "by" as your preposition will be correct in all cases - e.g. "I went to the city by plane/train/bus/boat." - and "by" is probably the most typical English usage.

"To get on" is another English construct that could be applied to all those modes of transport, but it simply means to set foot into.

Finally, if you're using the verb "to be", then "on" is the preposition to use in all cases - "I was on a plane/train/bus/boat when I heard the news."